note that in Jmol you can get the average B-factor using, for example:
print {:A}.temperature.average
and also get .stddev
On Mon, Jun 27, 2011 at 11:47 AM, Thomas Stout <thomasjstout@...>wrote:
>
> Hi Eric --
>
> I can't comment on how Jmol works out the B-factor color mapping, but I did
> want to comment on the comparing of B-factors amongst structures. The
> comparison of B-factors between structures is quite tricky. You absolutely
> CANNOT directly compare B-factors from one crystal structure to another.
> They are only valid within a single experiment. While a B-factor is
> ostensibly a "thermal parameter" and often interpretted to represent some
> measure of the "mobility" of an atom within a crystal, it is actually a
> measure of the certainty of atomic location, and in practice more of a scale
> factor. Many, many unmodeled sources of experimental error will get sopped
> up into this parameter, and it must not be construed as an absolute value.
> Within a single crystal structure, it is valid to compare B-factors since
> they have all been applied based on the same set of data and errors. Thus,
> if a loop has B-factors twice that of the core of the protein, it's pretty
> safe to say that that loop is more mobile. However, even the same
> structure, determined a second time from a second data set (all atoms being
> equal) cannot have its B-factors compared directly to those of the first
> structure since it arises from a different sample (crystal), different data
> collection and different data processing events. That said, there is a
> somewhat better argument for comparing relative B-factors between
> structures, but even that must be done with caution. For example, if you
> have two structures of the same protein in complex with different ligands
> (or, even a structure of Protein A and a site-mutant of the same protein),
> then you can reliably compare relative B-factors amongst the two
> structures... a statement like "the average B-factors of the backbone of
> loop 232-240 are 1.2X the average B-factor of structure "A", while the
> average B-factors of the backbone of loop 232-240 are 2X the average
> B-factor of structure "B"" would imply that there has been some causal
> disordering of that loop between structures "A" and "B".
>
> There is some literature out there on this, but it is probably more
> in-depth than is necessary....
>
> Cheers,
> Tom
>
>
>
> On Sun, Jun 26, 2011 at 9:01 PM, Eric Martz <emartz@...>wrote:
>
>> By experimentation, I have reached the following tentative
>> conclusions regarding the way Jmol maps colors in its
>> fixedTemperature and relativeTemperature color schemes:
>>
>> http://www.proteopedia.org/wiki/index.php/Temperature_color_schemes
>>
>> That page has several examples and buttons that allow you (via hover
>> reports: touch an atom with the mouse [don't click]) to ascertain
>> what temperature value is mapped to white.
>>
>> 1. I have been unable to deduce how Jmol determines the white value
>> for the relative temperature scheme. It is neither the average nor
>> the median temperature value. Can someone enlighten me?
>>
>> 2. Are the conclusions in my first table correct?
>>
>> 3. Are these points documented somewhere?
>>
>> 4. From the examples in my second table, comparing resolution to the
>> range and average temperature values, it appears to me that
>> temperature values or B factors are absolute, rather than relative.
>> If so, these values can be meaningfully compared between experiments.
>> Are there any crystallographers reading this who care to comment?
>>
>> Thanks, -Eric
>>
>>
>>
>> ------------------------------------------------------------------------------
>> All of the data generated in your IT infrastructure is seriously valuable.
>> Why? It contains a definitive record of application performance, security
>> threats, fraudulent activity, and more. Splunk takes this data and makes
>> sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-d2d-c2
>> _______________________________________________
>> Jmol-users mailing list
>> Jmol-users@...
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

it's just a straight scale from on end to the other. No weighting.
On Sun, Jun 26, 2011 at 11:01 PM, Eric Martz <emartz@...>wrote:
> By experimentation, I have reached the following tentative
> conclusions regarding the way Jmol maps colors in its
> fixedTemperature and relativeTemperature color schemes:
>
> http://www.proteopedia.org/wiki/index.php/Temperature_color_schemes
>
> That page has several examples and buttons that allow you (via hover
> reports: touch an atom with the mouse [don't click]) to ascertain
> what temperature value is mapped to white.
>
> 1. I have been unable to deduce how Jmol determines the white value
> for the relative temperature scheme. It is neither the average nor
> the median temperature value. Can someone enlighten me?
>
> 2. Are the conclusions in my first table correct?
>
> 3. Are these points documented somewhere?
>
> 4. From the examples in my second table, comparing resolution to the
> range and average temperature values, it appears to me that
> temperature values or B factors are absolute, rather than relative.
> If so, these values can be meaningfully compared between experiments.
> Are there any crystallographers reading this who care to comment?
>
> Thanks, -Eric
>
>
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

Hi Eric --
I can't comment on how Jmol works out the B-factor color mapping, but I did
want to comment on the comparing of B-factors amongst structures. The
comparison of B-factors between structures is quite tricky. You absolutely
CANNOT directly compare B-factors from one crystal structure to another.
They are only valid within a single experiment. While a B-factor is
ostensibly a "thermal parameter" and often interpretted to represent some
measure of the "mobility" of an atom within a crystal, it is actually a
measure of the certainty of atomic location, and in practice more of a scale
factor. Many, many unmodeled sources of experimental error will get sopped
up into this parameter, and it must not be construed as an absolute value.
Within a single crystal structure, it is valid to compare B-factors since
they have all been applied based on the same set of data and errors. Thus,
if a loop has B-factors twice that of the core of the protein, it's pretty
safe to say that that loop is more mobile. However, even the same
structure, determined a second time from a second data set (all atoms being
equal) cannot have its B-factors compared directly to those of the first
structure since it arises from a different sample (crystal), different data
collection and different data processing events. That said, there is a
somewhat better argument for comparing relative B-factors between
structures, but even that must be done with caution. For example, if you
have two structures of the same protein in complex with different ligands
(or, even a structure of Protein A and a site-mutant of the same protein),
then you can reliably compare relative B-factors amongst the two
structures... a statement like "the average B-factors of the backbone of
loop 232-240 are 1.2X the average B-factor of structure "A", while the
average B-factors of the backbone of loop 232-240 are 2X the average
B-factor of structure "B"" would imply that there has been some causal
disordering of that loop between structures "A" and "B".
There is some literature out there on this, but it is probably more in-depth
than is necessary....
Cheers,
Tom
On Sun, Jun 26, 2011 at 9:01 PM, Eric Martz <emartz@...>wrote:
> By experimentation, I have reached the following tentative
> conclusions regarding the way Jmol maps colors in its
> fixedTemperature and relativeTemperature color schemes:
>
> http://www.proteopedia.org/wiki/index.php/Temperature_color_schemes
>
> That page has several examples and buttons that allow you (via hover
> reports: touch an atom with the mouse [don't click]) to ascertain
> what temperature value is mapped to white.
>
> 1. I have been unable to deduce how Jmol determines the white value
> for the relative temperature scheme. It is neither the average nor
> the median temperature value. Can someone enlighten me?
>
> 2. Are the conclusions in my first table correct?
>
> 3. Are these points documented somewhere?
>
> 4. From the examples in my second table, comparing resolution to the
> range and average temperature values, it appears to me that
> temperature values or B factors are absolute, rather than relative.
> If so, these values can be meaningfully compared between experiments.
> Are there any crystallographers reading this who care to comment?
>
> Thanks, -Eric
>
>
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>

By experimentation, I have reached the following tentative
conclusions regarding the way Jmol maps colors in its
fixedTemperature and relativeTemperature color schemes:
http://www.proteopedia.org/wiki/index.php/Temperature_color_schemes
That page has several examples and buttons that allow you (via hover
reports: touch an atom with the mouse [don't click]) to ascertain
what temperature value is mapped to white.
1. I have been unable to deduce how Jmol determines the white value
for the relative temperature scheme. It is neither the average nor
the median temperature value. Can someone enlighten me?
2. Are the conclusions in my first table correct?
3. Are these points documented somewhere?
4. From the examples in my second table, comparing resolution to the
range and average temperature values, it appears to me that
temperature values or B factors are absolute, rather than relative.
If so, these values can be meaningfully compared between experiments.
Are there any crystallographers reading this who care to comment?
Thanks, -Eric